Callida Genomics (a majority owned subsidiary of Hyseq Pharmaceuticals), in collaboration with the Malaria Initiative Program at Harvard University School of Public Health, is developing universal DNA arrays for discovery and genotyping of drug resistance mutations in the malaria parasite Plasmodium falciparum. The process is based on Callida's Sequencing by Hybridization technology which is capable of routine whole gene sequencing and universal multiplex genotyping. Three prototype products will be developed and used by both Harvard and Callida's laboratories to sequence and genotype several genes in approximately 150 malaria patient samples with precisely characterized drug resistance levels. The project involves sequencing a total of 2.3 MB of malaria parasite DNA in order to discover new drug resistant mutations with high predictive efficiency. The project's long term objective is to optimize therapy and disease management procedures by developing an inexpensive and accurate diagnostic chip-based kit. The kit is designed to detect in a single assay all known drug resistant mutations of P. falciparum including new mutations discovered during this project. This innovative and efficient universal system can be used in any laboratory for rapid DNA sequence analysis of any pathogen DNA for multiple research, diagnostic and biodefense applications.